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CpG interval report generated on 20/05/20 with pycoMeth 0.4.6
Interval details
| pvalue rank | chromosome | start | end | length | number of samples | number of CpGs | pvalue | adjusted pvalue |
|---|---|---|---|---|---|---|---|---|
| #5 | 1 | 145167533 | 145169830 | 2297 | 3 | 76 | 1.62265e-31 | 3.22744e-28 |
Methylation log-likelihood ratio by CpG position
Distribution of CpG methylation log-likelihood ratio by sample
Closest transcripts TSS
| distance to tss | transcript id | gene id | transcript name | chromosome | start | end | strand | feature type | transcript biotype |
|---|---|---|---|---|---|---|---|---|---|
| 0 | enst00000621562 | sg00000277678 | rnu1-153p-201 | 1 | 145169519 | 145169664 | + | snRNA | snrna |
| 0 | enst00000578899 | sg00000272419 | linc01145-202 | 1 | 145164099 | 145168712 | - | lnc_RNA | processed_transcript |
| -45 | enst00000621033 | sg00000272419 | linc01145-207 | 1 | 145164100 | 145167488 | - | lnc_RNA | retained_intron |
| -27547 | enst00000640951 | sg00000283752 | ac241585.3-201 | 1 | 145139986 | 145148375 | + | pseudogenic_transcript | unprocessed_pseudogene |
| 45021 | enst00000638358 | sg00000281571 | ac241585.2-201 | 1 | 145214851 | 145215905 | + | unconfirmed_transcript | tec |
| 45021 | enst00000628937 | sg00000281571 | ac241585.2-202 | 1 | 145214851 | 145215938 | + | unconfirmed_transcript | tec |
| 45896 | enst00000638217 | sg00000272419 | linc01145-209 | 1 | 145214677 | 145215726 | - | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| 45916 | enst00000418192 | sg00000272419 | linc01145-201 | 1 | 145201188 | 145215746 | - | lnc_RNA | processed_transcript |
| 45984 | enst00000610324 | sg00000272419 | linc01145-204 | 1 | 145169036 | 145215814 | - | lnc_RNA | processed_transcript |
| 45984 | enst00000614510 | sg00000272419 | linc01145-205 | 1 | 145168421 | 145215814 | - | lnc_RNA | processed_transcript |
| 46020 | enst00000606004 | sg00000272419 | linc01145-203 | 1 | 145168405 | 145215850 | - | lnc_RNA | processed_transcript |
| 46042 | enst00000616993 | sg00000272419 | linc01145-206 | 1 | 145200691 | 145215872 | - | lnc_RNA | processed_transcript |
| 46228 | enst00000621798 | sg00000272419 | linc01145-208 | 1 | 145164099 | 145216058 | - | lnc_RNA | processed_transcript |
| 63171 | enst00000433527 | sg00000223612 | ac241585.1-201 | 1 | 145233001 | 145233519 | + | pseudogenic_transcript | processed_pseudogene |
| -71559 | enst00000400889 | sg00000215784 | fam72d-201 | 1 | 145095974 | 145112696 | + | mRNA | protein_coding |
| -72005 | enst00000641863 | sg00000196369 | srgap2b-207 | 1 | 144892021 | 145095528 | - | mRNA | protein_coding |
| -72005 | enst00000612199 | sg00000196369 | srgap2b-204 | 1 | 144887265 | 145095528 | - | mRNA | protein_coding |
| -72007 | enst00000463366 | sg00000196369 | srgap2b-201 | 1 | 145093043 | 145095526 | - | lnc_RNA | processed_transcript |
| 72294 | enst00000544708 | sg00000256374 | ppial4d-201 | 1 | 145241630 | 145242124 | - | mRNA | protein_coding |
| -72554 | enst00000467933 | sg00000196369 | srgap2b-202 | 1 | 145092987 | 145094979 | - | lnc_RNA | processed_transcript |
| -72568 | enst00000494534 | sg00000196369 | srgap2b-203 | 1 | 145093053 | 145094965 | - | lnc_RNA | processed_transcript |
| -74287 | enst00000619678 | sg00000196369 | srgap2b-205 | 1 | 144892049 | 145093246 | - | mRNA | protein_coding |
| 100060 | enst00000603689 | sg00000271291 | ac245014.2-201 | 1 | 145269604 | 145269890 | - | pseudogenic_transcript | processed_pseudogene |
| 111286 | enst00000618589 | sg00000276216 | ac245014.3-201 | 1 | 145281116 | 145281462 | + | lnc_RNA | lncrna |
| 111286 | enst00000384770 | sg00000207501 | rnvu1-14-201 | 1 | 145281116 | 145281279 | + | snRNA | snrna |
| 117925 | enst00000427732 | sg00000236140 | ac245014.1-201 | 1 | 145286610 | 145287755 | - | lnc_RNA | lncrna |
| -202508 | enst00000604134 | sg00000271644 | ac242498.1-201 | 1 | 144965025 | 144965135 | + | pseudogenic_transcript | processed_pseudogene |
| -212087 | enst00000621582 | sg00000196369 | srgap2b-206 | 1 | 144897236 | 144955446 | - | mRNA | nonsense_mediated_decay |
| 233473 | enst00000622803 | sg00000162825 | nbpf20-205 | 1 | 145290620 | 145403303 | - | mRNA | protein_coding |
| 233473 | enst00000594479 | sg00000162825 | nbpf20-203 | 1 | 145290639 | 145403303 | - | mRNA | protein_coding |
| 235615 | enst00000620821 | sg00000162825 | nbpf20-204 | 1 | 145291500 | 145405445 | - | mRNA | protein_coding |
| 235737 | enst00000369373 | sg00000162825 | nbpf20-201 | 1 | 145289900 | 145405567 | - | mRNA | protein_coding |
| 235948 | enst00000392971 | sg00000162825 | nbpf20-202 | 1 | 145289900 | 145405778 | - | mRNA | protein_coding |
| 237942 | enst00000443612 | sg00000234367 | pfn1p3-201 | 1 | 145407772 | 145408173 | + | pseudogenic_transcript | processed_pseudogene |
| 261863 | enst00000580816 | sg00000270384 | rnu1-154p-201 | 1 | 145431527 | 145431693 | - | snRNA | snrna |
| 289968 | enst00000664012 | sg00000286620 | ac239860.3-201 | 1 | 145459798 | 145462007 | + | unconfirmed_transcript | tec |
| 295950 | enst00000605806 | sg00000270722 | rnvu1-31-201 | 1 | 145465617 | 145465780 | - | snRNA | snrna |
| 305776 | enst00000657459 | sg00000287374 | ac239860.4-201 | 1 | 145475606 | 145480999 | + | lnc_RNA | lncrna |
| 337614 | enst00000525886 | sg00000278182 | ac239860.2-201 | 1 | 145507444 | 145508607 | + | pseudogenic_transcript | unprocessed_pseudogene |
| 339217 | enst00000444680 | sg00000275064 | ac239860.1-201 | 1 | 145509047 | 145520594 | + | pseudogenic_transcript | unprocessed_pseudogene |
| -369901 | enst00000654923 | sg00000287607 | fp700111.3-201 | 1 | 144797534 | 144797632 | - | pseudogenic_transcript | processed_pseudogene |
| -380927 | enst00000619190 | sg00000273825 | fp700111.2-201 | 1 | 144754572 | 144786606 | - | pseudogenic_transcript | unprocessed_pseudogene |
| 421230 | enst00000606775 | sg00000272150 | nbpf25p-201 | 1 | 145573965 | 145591060 | - | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| 438028 | enst00000619932 | sg00000272150 | nbpf25p-202 | 1 | 145572345 | 145607858 | - | lnc_RNA | processed_transcript |
| 438158 | enst00000313835 | sg00000117262 | gpr89a-201 | 1 | 145607988 | 145670650 | + | mRNA | protein_coding |
| 438160 | enst00000460277 | sg00000117262 | gpr89a-202 | 1 | 145607990 | 145670463 | + | mRNA | nonsense_mediated_decay |
| 438189 | enst00000532574 | sg00000117262 | gpr89a-212 | 1 | 145608019 | 145623224 | + | lnc_RNA | retained_intron |
| 438197 | enst00000528944 | sg00000117262 | gpr89a-211 | 1 | 145608027 | 145647218 | + | mRNA | nonsense_mediated_decay |
| 438203 | enst00000466593 | sg00000117262 | gpr89a-205 | 1 | 145608033 | 145647236 | + | mRNA | nonsense_mediated_decay |
| 438218 | enst00000524525 | sg00000117262 | gpr89a-209 | 1 | 145608048 | 145618351 | + | mRNA | nonsense_mediated_decay |
| 438218 | enst00000534502 | sg00000117262 | gpr89a-213 | 1 | 145608048 | 145670184 | + | mRNA | protein_coding |
| 438783 | enst00000462900 | sg00000117262 | gpr89a-203 | 1 | 145608613 | 145670178 | + | mRNA | protein_coding |
| 441636 | enst00000527989 | sg00000117262 | gpr89a-210 | 1 | 145611466 | 145623714 | + | lnc_RNA | processed_transcript |
| 460857 | enst00000478703 | sg00000117262 | gpr89a-206 | 1 | 145630687 | 145663419 | + | lnc_RNA | processed_transcript |
| 460884 | enst00000492401 | sg00000117262 | gpr89a-207 | 1 | 145630714 | 145645928 | + | lnc_RNA | retained_intron |
| -466374 | enst00000410922 | sg00000222854 | rna5sp59-201 | 1 | 144701050 | 144701159 | - | pseudogenic_transcript | rrna_pseudogene |
| 474256 | enst00000493684 | sg00000117262 | gpr89a-208 | 1 | 145644086 | 145670460 | + | lnc_RNA | retained_intron |
| 476414 | enst00000465185 | sg00000117262 | gpr89a-204 | 1 | 145646244 | 145670463 | + | lnc_RNA | retained_intron |
Source file: /hps/research1/birney/users/adrien/analyses/cancer_DNA_promethion/run_1_2_3_4/DNA_pipeline_2/results/methylation/pycometh_meth_comp_CGI_3/out.tsv.gz
MD5 hash: 9aa0e3f69cb4e12345c3758eb68a5efc